very interesting.....at first, i think this is a special case (genetic mosaicism).
however, after very quick research, i think may be it is not that uncommon than I originally thought....
then, i try to find the fundamentals definition of male and female and seems cannot find a very concrete definition.....very interesting indeed.
however, when i think about it, for example, for cancer patients, their also experienced genome instability. Then, from this point of view, it is possible that some of our cells, at this very moment might have different chromosome than the others?
(ofcourse, for XY genotype, Y deletion is possible. but I suppose people with XX genotype cannot create a Y chromosomes from thin air?)
imo, for the function of the society and simplicity.
it is better than sex remain "biological" condition while gender remain a "social" condition.
in your case, I think it can still count as a special case and allow him/her to decide the biological sex. (afterall, biologically speaking, there are genetic defects).
however, you also need to consider that the liquidity of gender identification also created different social problems (eg. sport events / social distress of different gender individuals in the toilet).